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Improve gut health with a microbiome diet

What is the microbiome?

You may not be aware, but there are millions of bacteria living inside your gut. This bacteria is also known as your microbiome or your gut flora. Everyone’s microbiome is unique to them and is shaped by many factors including our genetics and DNA. Studies on twins have shown that family members share common gut flora which could affect how much body weight we gain and where we store it1.

What is bacteria?

Bacteria are tiny living organisms – usually consisting of just one cell – that can be found just about anywhere, including in our guts! Most bacteria are ‘good’ and help our body perform certain tasks. However, some are ‘bad’ and can cause infections and illness.

The key is to strike a balance between good and bad bacteria that live in the gut. Researchers say that when gut bacteria becomes out of balance, it can cause health issues which may lead to an increased risk of conditions like heart disease, cancer and type 2 diabetes2. On the Huffington Post blog, Raphael Kellman, MD author of The Microbiome Diet explains: “When your microbiome is balanced, you have a terrific ally that keeps your body healthy, promoting good digestion, clear thinking, balanced mood, and glowing overall health. When your microbiome goes out of balance, however, you risk such symptoms as brain fog, depression, anxiety, bad skin and insomnia — and, down the road, obesity, diabetes, and cancer.”3

How does your diet affect the microbiome?

What we eat can have a big impact on the health of our gut and our individual microbiome can affect our metabolism, digestion and weight. A large study in the Netherlands found that everything we drink or eat has an effect on the bacteria living in our digestive systems as well as our overall health4. Other evidence suggests that a diet high in sugar and fat changes the bacteria in the microbiome and leads to obesity5. So, to keep our microbiomes healthy, a varied diet is essential. Researchers believe that a diverse diet leads to a diverse microbiome that is able to deal with any bacteria that is harmful to your health6.

What is a microbiome diet?

The idea is to eat a diet full of  foods which helps support levels of  good bacteria in your gut. A healthy gut diet plan is full of whole foods and nutrients – basically foods that help your digestive system work at its best - and less processed and harder-to-digest foods. These foods can include:

Fruit and vegetables

Packed with essential vitamins, minerals and dietary fibre, getting your 5 a day is essential for a healthy, balanced microbiome. Aim to fill your plate with a variety of fresh fruit and veg like broccoli, spinach, carrots, blueberries, apples and strawberries.

Herbs and spices

Flavour your food with aromatic spices like ginger and turmeric. Both are known for managing inflammatory responses in the body.

Friendly bacteria

Foods that contain friendly bacteria may help restore good bacteria in your gut and keep it healthy7. In fact, the Netherlands study found that people who regularly ate yoghurt had more diverse gut bacteria. As well as yoghurt, fermented foods like kefir, miso or kombucha also contain friendly bacteria.


Evidence suggests that Omega-3 fatty acids helps inflammation in the body8. To get your fill, go for oily fish like salmon or tuna, chia seeds or flaxseeds.


According to research, whole grains aren’t just a nutritious way to provide your body with digestive-friendly fibre, they could also improve the balance of bacteria in your microbiome9. Staple wholegrains of a gut health diet include: porridge oats, brown rice, quinoa, bulgur wheat, barley, popcorn, whole-wheat bread and buckwheat. These hearty grains may also keep you feeling fuller for longer.

Red wine

In moderation, red wine could help keep your microbiome diverse. It contains resveratrol, which one study found may lessen the risk of heart disease by adapting the gut microbiome10.

What foods should you avoid on a microbiome diet?


Research shows that drinking excessively or for long periods may affect the microbiome which could, in turn, lead to liver disease11.

Refined carbohydrates

Evidence shows that eating refined carbohydrates on a regular basis could have an inflammatory effect on the body12. Instead, cut down on white bread and pasta in favour of whole grains, which are much better for a good gut health diet.

Hydrogenated fat

Research suggests that processed food that contains hydrogenated (trans) fat may cause inflammation13. These foods are also often high in calories, which may decrease the diversity of our gut bacteria14.

Making some changes to your diet helps support your microbiome, but remember that there is no “one size fits all” approach.  “But there is a good correlation between diversity and health: greater diversity is better,” researcher Alexandra Zhernakova MD PhD says. And Dr Kelleman agrees: “The key is to keep supporting your little friends inside — your microbiome.”

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Last updated: 22 May 2020